Temperance, much like River, shows an intellect that makes everyone else look like an idiot child, she's an expert shot (The Wannabe In The Weeds, she shoots Booth's stalker through her throat with only a quick look, and nobody ever actually said that River was trained in firearms, plus the fact that she stated herself that she just did the math), and genetics don't argue against it. Also, she could see Teddy's ghost, so perhaps it was some low level psychic powers. Plus, it could actually happen, both being Fox shows and all.

Adding on, it's not too much of a stretch that if the Tams descended from Brennan, maybe a certain Genki Girl mechanic is the descendant of a certain Genki Girl squintern (and, by extent, a certain plucky psychologist).

And maybe Mal is descended from Booth as well, through Parker. Wash through Hodgins and Angela. Book through Caroline. Inara through Arastoo. Zoe through Wendell. Jayne through Fisher. Yes, this troper actually thought about this.

C'mon what modern present day Forensics lab has a Holographic facial reconstruction device to SO many touch screen capable (both mounted and handheld) devices for standard equipment??

none of them, it's not standard, it's called the ANGELAtron for a reason, she's a computer genius and made it herself

Hodgins is a spy.

After all, if the US Government wanted someone to spy on the lab, it would be logical to use a conspiracy theorist. Nobody expects conspiracy theorists to be an active part of government conspiracies.

Naw, the spy is the Cuban intern

His back-story is similar to Aristoo's — intellectual family in a repressive country, loads of family trauma due to said repressive country, has great affection for religion (he isn't Catholic but his father was and he keeps his cross as a memento), comes to America and (tries) to hook up with his boss — the problem is that Aristoo's story is told over several episodes while the Cuban guy tells and does all of this in his first appearance which is kind of overwhelming. Plus there's the fact that no one finds him suspicious (unlike the blonde guy who everyone thought was in debt to gangsters or the redneck guy who only became interested in criminal science because he wanted to kill his abusive step-dad (he didn't, but he scared his step-dad so much that he ditched the family without leaving a trace so everyone assumed he did)) and he's immediately accepted (hitting on Bones notwithstanding; the official government endorsement also helps ease their minds).

Sweets was Gormogon's real apprentice.

The case for Sweets just fits too well, and the case for Zach is stretched a little too thin. And, canonically, Zach never killed anyone.

Sweets showed up at the right time, threw a small monkey wrench into the Gormogon case, and pegged Zach as the perfect patsy. And now Sweets is Zach's therapist, keeping him from confessing too much.

The secret societies in the government know that the apprentice wasn't really killed. That's why they ran the Jeffersonian labs through that thing in the JFK episode "The Proof in the Pudding" that Sweets identified as a psychological test.

Something tells me that

A) That a writer for Bones is a Troper, and

B) This isn't correct, as it was even mocked in the S4F, "The End in the Beginning".

Sweets: Um, I mean the name of the band is Gormogon. Some people think I'm Gormogon, but I'm not.

A) this theory was added after the season 4 finale

B) You say "mocked," I say "reiterated." They addressed the fact that in the season 3 finale where they discover Zach is Gormogon's apprentice, Sweets was one of the suspects. This is their way of reminding us of that so that, if this theory is correct, it doesn't come out of left field.

Jossed. Word Of God said that originally they had planned for Sweets to be Gormogon, but that the Writer's Strike derailed the plot, so they scrapped it, and that the Season 4 finale line was a joke. Also, after four seasons I don' t think they'll change that. :)

It explains why he was able to escape from the Gravedigger, and how Brennan was able to see Parker in the Cemetery. Booth subconsciously projected the image and voice of Corporal Parker into Brennan's mind.

Booth is not Catholic, or is a severely lapsed Catholic

It seems in character for him to play up his religious background when Bones gets into her more Hollywood Atheist moments to remind her that people don't share her worldview and not to let here worldview interfere with the case.

Note that he seems okay with the idea of ghosts. The Roman Catholic Church isn't.

Then again, how many people, Catholic or non-Catholic, actually know the Church's position on the existence of ghosts?

I'm an alter server and I believe in ghosts.

The views of the church aren't necessarily the views of the individual, but that doesn't make the beliefs of either less Catholic (or whatever other religion)

He's dead, and clearly not a hallucination because he interacted with physical objects in a way Booth couldn't've. Plus, Booth looks a lot like Angel.

But the First can't interact with physical objects, either.

Hmm, that does make sense, but who's to say he actually did that? Perhaps he gave Booth a power boost for a bit and made it look like he was doing it.

Temperance is a poorly-programmed but incredibly lifelike android sent here by aliens to study humans.

She studies bones to understand the physical aspect. "I don't know what that means" is her response to learning about the cultural aspect. This theory was brought up by Sweets in his Character Blog entry for the episode "The Finder."

The Shansu eventually came true, he became human and adopted the identity of Seeley Booth. He has a lot of experience solving mysteries.

Brennan's niece is a Werewolf.

It's true in the book series now, at any rate.

Micah, the security guard who appears in "The Doctor in the Photo", is Brennan's hallucination.

Brennan only sees Micah when she is alone.

Brennan says she understands what he is saying more easily than she understands anyone else.

Despite that and in the many years they've worked together, she has never mentioned him to Booth until that very episode.

The biggest issue I see with this plot is that they already did it with Booth.

Seeing as the show likes to throw in the occasional Not So Different moment, this might actually be a point for.

His line about how Bones "doesn't normally talk to herself" was especially telling to me. She doesn't talk to herself... because she normally visualizes him and does it that way.

Additionally, this episode explicitly shows Bones interpreting reality differently this episode (seeing the victim as looking identical to her). Granted it's not on the same scale as visualizing a dude, but it does create precedence that she's not exactly reliable.

Micah the security guard is a ghost

Expanding on the theory above, who else would have all that free time to go to lectures AND be a night guard? Also, no one else seems to know who he is, and Brennan is already talking to one dead person in the episode. Granted, "Bones" doesn't often deal with the supernatural, but this is WMG, it's meant to be fun.

Except that, at least sometimes, it does. There are all sorts of Supernatural things (Like the Witch's ghost) that get half-explained by the show, but still make more sense if viewed as Supernatural. Micah definitely seems to count.

For all it's worth, Micah means "Who is like God?" and is certainly not the most common name amongst security guards. It fits both as a Meaningful Name if he's something supernatural, and a Cool Name a writer like Brennan would make up, if he is a figment of her imagination.

Or maybe he is her guardian, he had a really sweet friendship with her.

The Gormogon's final apprentice was black-mailed into working for him

Zack was kidnapped at somepoint during season 3 by the Gormogon. He offered him a choice; a) become his new apprrentice to do his bidding and spy on the Jeffersonian or b) be killed and eaten. Zack refused, but the Gormogon then threatened to kill Hodgins if he didn't help him, leaving Zack without much of an option. And to make sure Zack didn't reveal what was happening, the Gormogon kept the threat on Hodgins' life as his black-mail material. Even after the Gormogon is killed, Zack is too scared to come forwards, still afraid someone will try and kill him, so he takes the heat.

Expansion: Zack has good reason to be afraid. Traditionally, 'Gormogon' was not the only member of the society. We're told in the show that there's only the one pair left, but, we don't actual have any evidence this is the case. They were a whole secret society after all.

There is a long running Myth Arc going on deep in the background of Bones involving the supernatural.

We're supposed to just handwave all the things that we see or are implied away, but in the Last Season it will turn out to be incredibly important.

Namely, the barriers between the living and dead have been growing weaker over the series and the weakest point is in the Jeffersonian. By the final season this rift will be reaching a breaking point. This will mean either a) the ghosts will try and repair it with the help of the Squints or b) Zombie Apocalypse .

Hodgins is Batman.

He's insanely rich, so he has the resources to pull it off. Not to mention that he's definetly a little bit crazy, which anyone would have to be to become Batman.

Would that make Zack Robin?

That would explain why Zack and Hodgins live together.

And Zack just seems like sidekick material.

Or it could possibly be Sweets. Hodgins one referred to him as a sidekick and they've been on a "secret mission" together.

That was the time Angela's dad made Hodgins get his car back as a test of character. Sweets just tagged along.

Maybe that was a test of character for Sweets too, except from Hodgins instead of Billy Gibbons. He wanted to see if he'd make a good sidekick.

Come on guys, there's more than one Robin. Zack was the first and then when he got locked up Hodgins bonded with Sweets and let him become Robin. If Zack was to ever return he'd become Nightwing or Red Robin.

"Bones" is an alternate DC universe

Inspired by the WMG above. The situation is either a) Squints are the Justice League in this universe, albeit, a more literal one, or b) They are alternate versions of the superheroes. Hodgins, as stated above, is Batman, Zack and Sweets are Robin (the latter replacing the former after the whole Gormogon mess), Brennan is Wonder Woman (she already has the costume), Cam is Catwoman (Again, costume) and Booth is Superman.

Wendell could be another Robin.

What would that make Angela?

Maybe all the Squinters take turns being Robin.

Angela would either be Batwoman or Harley Quinn.

Or Talia. She and Batman did have a kid together.

And if Angela is Talia, that would mean Billy Gibbons is...

Billy Gibbons. There is no superhero mightier than him.

Also, Daisy would be Harley Quinn.

If we go into villains, Howard Epps would be the Joker.

That EMT who scared girls to death in season 3 could be Scarecrow.

The Gravedigger would probably be Poison Ivy or The Riddler.

The Jeffersonian is part of The SCP Foundation

It's a well funded organization with quirky scientists and we know they also have a large amount of artifacts in storage (what with it being based off the Smithsonian and all). Maybe it's a storage and research facility for them?

Brennan will become pregnant.

Since Emily Deschanel is now expecting her first child, we can presume Brennan may also end up expecting a little Squint, possibly reviving the plot thread from the end of season 4.

Confirmed. Brennan is pregnant and Booth is the father.

Bones became pregnant in the first truly emotional decision she's ever made.

It's implausible that she just forgot to stay on the pill or fish out one of Booth's unused condoms. She wanted to get pregnant so that if something happened to one of them (not hard to imagine), the other would have someone to remember them by.

Brennan's understanding of idioms and social mores tends to swing wildly, especially as the seasons go on. This is because her own personal problems (let's face it, she's got Asperger's) combined with the stress of her work are taking their toll.

Oddly enough, it's making her more humanistic, rather than more Data-like.

This is basically canon. She essentially confessed her love for Booth and broke down crying after being rejected in "The Doctor in the Photo". That whole episode is about Brennan realising her fear of real relationships and emotional connections is a flaw rather than a strength. This is either Character Development or Character Derailment depending on your perspective.

Hodgins had Goodman fired.

He pulled his influence and had him dismissed after one argument too many.

If Goodman threatened to fire Hodgins (or someone else that Hodgins feels close to, like Zack or Angela), then it's possible Hodgins would have had a few strings pulled behind the scenes to have Goodman replaced.

Again, inspired by the WMG above. It's not too hard to imagine paranoid conspiracy theorists run in the Hodgins family. Plus, maybe his Uncle Booth rubbed off on him. Because this is WMG, lets ignore the huge time/name/everything else flaws.

Adding on, it's not too much of a stretch to assume Booth and Brennan's baby, if it's a girl, growing up to becoming Agent Scully.

Or, they could grow up to be X-Files: The Next Generation. Come on, you know you want it. They could tie up all the WTF dangling threads from the original...And it might just be worth it for the possibility of seeing an older Doggett passing down wisdom to the next generation.

This should happen. Although I'd have it with Hodgins and Sweets as Back-to-Back Badasses in a heroic last stand. Other than that...Seems like a logical thing to air mid-season just to lighten it up a bit. Could even have old cases come back to haunt them.

Brennan will lose the baby

It seems like it would mess up the show a bit. Brennan seems unlikely to have the child then leave it at home the whole time she's at her (very time-consuming) job. They're also not going to show her having an abortion, so it seems likely that during some case or other, she's going to be injured in a non-permanent way that nevertheless costs her the child.

Practical for the show, given that writing the baby in in any meaningful capacity would be tricky, and the loss would provide good emotional trauma as an excuse to keep her and booth separate for a bit longer, and continue the long-running UST without awkward break-up episodes.

Given that the show is as much about Brennan's evolution as a person as it is about the cases, having a miscarriage this far along, which would just serve to undo all her Character Development, smacks of a Diabolus Ex Machina. More likely, she'll have a close call, which will cause her to stop intellectualizing and truly consider her impending motherhood.

Jossed. They found an even dumber way to break them up.

Brennan will have an impaired baby

Brennen assumes that any child she has will be exceptional, but she will end up with an intellectually and/or physically challenged child and have to cope with that.

We know that Booth's grampa and Gibbs' dad are the same actor. It does explain why Booth is so Badass and such a good sniper.

Sully will return and want Bones back.

For whatever reason, Sully will come back from Jamaica and want to get back together with Bones. Which will create tension now that she and Booth are together and end with Booth and Sully dukin out. Brought to you by a person who believes Sully is a relationship sue.

In the final Pelant episode, Zack will save the day.

Think about it! Pelant is a genius computer hacker, but Zack is genius on an even higher scale. Brennen or Hodgins will eventually go to him for help on dealing with Pelant, and Zack will be able to find the clues the team needs to finally take him down.

Jossed. Zack isn't even mentioned in the final Pelant episode.

We'll be saying good-bye to another Squintern in the final Pelant episode.

Remember, during the previous arc against Broadsky, Vincent was killed. And during the Gormogon Arc, Zack was written out of the story. Keeping in tradition, Pelant will probably end up killing one of the Squinterns, finally pushing Booth over the edge and killing the bastard.

Nope! Booth doesn't give him the chance.

One of the girls from "The Girl in the Curl" will make a reappearance.

She will have been inspired to become a forensic anthropologist by Dr. Brennan, who showed her that a woman could be smart and beautiful, and comes back almost 10 years later to than her for being such a good role model.

Seeley Booth inherited his Pop's love of Big Beautiful Women, but he also happens to be very much into a woman's intellect and personality. The women we see him date are generally slender because the women he has dated during the show's run just all happened to catch his eye for their intelligence and charm while not having the fuller figure he usually prefers. His feelings for Bones stop him from admitting his preference for big women because she's slim and he thinks it's unlikely that she would want to gain weight. During The Foot In The Foreclosure he plays the standard devil's advocate role, because Brennan isn't. Pops declares that "There's nothing wrong with a bit of jello in your jam," because he thinks that Booth is just too embarrassed to admit that he likes big girls. He's been aware of Booth's preference for big women ever since Booth was going through puberty and started paying way more attention to his fatter classmates than the school cheerleaders.

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